Example: Analyzing a yeast data set

Next generation sequencing (NGS) is one of the most powerful technologies we have to gather data on biological samples. While it is used to determine genetic content and to assay RNA abundance, it is also used in combination with diverse protocols to investigate DNA/RNA binding proteins or to assess the composition of non-clonal or metagenomic populations. In clinical settings NGS is used to screen for novel drugs, drug targets, or essential genes; it has also been proposed as an advanced, if expensive, diagnostic tool.

In this guideline we present the NGS module for Qlucore Omics Explorer (QOE), a general all-purpose module designed to facilitate the analysis of such diverse NGS experiments as listed above and complement the powerful tools already included in QOE in a seamless way. This guideline will demonstrate the NGS module in a step-by-step manner so that the reader may follow along. Through each step, the reader will be introduced to core concepts of any NGS pipeline. These steps will include ideas from data preparation, quality control, and genomic annotation through to statistical inference and exploratory data analysis. Along the way, we introduced the new genome browser included within the NGS module. The genome browser is a powerful visual tool to quickly assess concepts such as alignment quality, mappability, disproportionate mapping along CDS regions, transcription start and stop sites, splice forms, and genetic variants within the context of known or custom genomic features.

The essential advantage of a genome browser is that it allows us to observe NGS results as continuous functions rather than as discrete summarizations of genomic regions, such as brought about by RPKM normalizations and other similar summaries. The NGS module therefore allows users of QOE to work in and take advantage of both spaces in a synchronized way.

Category: Application notes